Technical University of Denmark

About: Technical University of Denmark is a education organization based out in Kongens Lyngby, Hovedstaden, Denmark. It is known for research contribution in the topics: Population & Catalysis. The organization has 24126 authors who have published 66394 publications receiving 2443649 citations. The organization is also known as: Danmarks Tekniske Universitet & DTU.

ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites.

Abstract: We present a neural network based method (ChloroP) for identifying chloroplast transit peptides and their cleavage sites. Using cross-validation, 88% of the sequences in our homology reduced training set were correctly classified as transit peptides or nontransit peptides. This performance level is well above that of the publicly available chloroplast localization predictor PSORT. Cleavage sites are predicted using a scoring matrix derived by an automatic motif-finding algorithm. Approximately 60% of the known cleavage sites in our sequence collection were predicted to within +/-2 residues from the cleavage sites given in SWISS-PROT. An analysis of 715 Arabidopsis thaliana sequences from SWISS-PROT suggests that the ChloroP method should be useful for the identification of putative transit peptides in genome-wide sequence data. The ChloroP predictor is available as a web-server at http://www.cbs.dtu.dk/services/ChloroP/.

Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence.

Abstract: Post-translational modifications (PTMs) occur on almost all proteins analyzed to date. The function of a modified protein is often strongly affected by these modifications and therefore increased knowledge about the potential PTMs of a target protein may increase our understanding of the molecular processes in which it takes part. High-throughput methods for the identification of PTMs are being developed, in particular within the fields of proteomics and mass spectrometry. However, these methods are still in their early stages, and it is indeed advantageous to cut down on the number of experimental steps by integrating computational approaches into the validation procedures. Many advanced methods for the prediction of PTMs exist and many are made publicly available. We describe our experiences with the development of prediction methods for phosphorylation and glycosylation sites and the development of PTM-specific databases. In addition, we discuss novel ideas for PTM visualization (exemplified by kinase landscapes) and improvements for prediction specificity (by using ESS--evolutionary stable sites). As an example, we present a new method for kinase-specific prediction of phosphorylation sites, NetPhosK, which extends our earlier and more general tool, NetPhos. The new server, NetPhosK, is made publicly available at the URL http://www.cbs.dtu.dk/services/NetPhosK/. The issues of underestimation, over-prediction and strategies for improving prediction specificity are also discussed.

Alternative Plasmonic Materials: Beyond Gold and Silver

Abstract: Materials research plays a vital role in transforming breakthrough scientific ideas into next-generation technology. Similar to the way silicon revolutionized the microelectronics industry, the proper materials can greatly impact the field of plasmonics and metamaterials. Currently, research in plasmonics and metamaterials lacks good material building blocks in order to realize useful devices. Such devices suffer from many drawbacks arising from the undesirable properties of their material building blocks, especially metals. There are many materials, other than conventional metallic components such as gold and silver, that exhibit metallic properties and provide advantages in device performance, design flexibility, fabrication, integration, and tunability. This review explores different material classes for plasmonic and metamaterial applications, such as conventional semiconductors, transparent conducting oxides, perovskite oxides, metal nitrides, silicides, germanides, and 2D materials such as graphene. This review provides a summary of the recent developments in the search for better plasmonic materials and an outlook of further research directions.

Defining Uncertainty: A Conceptual Basis for Uncertainty Management in Model-Based Decision Support

Abstract: The aim of this paper is to provide a conceptual basis for the systematic treatment of uncertainty in model-based decision support activities such as policy analysis, integrated assessment and risk assessment. It focuses on the uncertainty perceived from the point of view of those providing information to support policy decisions (i.e., the modellers’ view on uncertainty) – uncertainty regarding the analytical outcomes and conclusions of the decision support exercise. Within the regulatory and management sciences, there is neither commonly shared terminology nor full agreement on a typology of uncertainties. Our aim is to synthesise a wide variety of contributions on uncertainty in model-based decision support in order to provide an interdisciplinary theoretical framework for systematic uncertainty analysis. To that end we adopt a general definition of uncertainty as being any deviation from the unachievable ideal of completely deterministic knowledge of the relevant system. We further propose to discriminate among three dimensions of uncertainty: location, level and nature of uncertainty, and we harmonise existing typologies to further detail the concepts behind these three dimensions of uncertainty.We propose an uncertainty matrix as a heuristic tool to classify and report the various dimensions of uncertainty, thereby providing a conceptual framework for better communication among analysts as well as between them and policymakers and stakeholders. Understanding the various dimensions of uncertainty helps in identifying, articulating, and prioritising critical uncertainties, which is a crucial step to more adequate acknowledgement and treatment of uncertainty in decision support endeavours and more focused research on complex, inherently uncertain, policy issues.

Electronic structure calculations with GPAW: a real-space implementation of the projector augmented-wave method

Abstract: Electronic structure calculations have become an indispensable tool in many areas of materials science and quantum chemistry. Even though the Kohn-Sham formulation of the density-functional theory (DFT) simplifies the many-body problem significantly, one is still confronted with several numerical challenges. In this article we present the projector augmented-wave (PAW) method as implemented in the GPAW program package (https://wiki.fysik.dtu.dk/gpaw) using a uniform real-space grid representation of the electronic wavefunctions. Compared to more traditional plane wave or localized basis set approaches, real-space grids offer several advantages, most notably good computational scalability and systematic convergence properties. However, as a unique feature GPAW also facilitates a localized atomic-orbital basis set in addition to the grid. The efficient atomic basis set is complementary to the more accurate grid, and the possibility to seamlessly switch between the two representations provides great flexibility. While DFT allows one to study ground state properties, time-dependent density-functional theory (TDDFT) provides access to the excited states. We have implemented the two common formulations of TDDFT, namely the linear-response and the time propagation schemes. Electron transport calculations under finite-bias conditions can be performed with GPAW using non-equilibrium Green functions and the localized basis set. In addition to the basic features of the real-space PAW method, we also describe the implementation of selected exchange-correlation functionals, parallelization schemes, Delta SCF-method, x-ray absorption spectra, and maximally localized Wannier orbitals.